User: Dattatray Mongad
Dattatray Mongad • 240
- Reputation:
- 240
- Status:
- Trusted
- Location:
- National Centre for Cell Science, Pune
- Website:
- http://www.nccs.res.in/
- Twitter:
- DattatrayMongad
- Last seen:
- 2 days, 19 hours ago
- Joined:
- 2 years, 3 months ago
- Email:
- d************@gmail.com
Posts by Dattatray Mongad
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3
votes
2
answers
170
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... **use biopython:**
from Bio import SeqIO
for records in SeqIO.Parse("fastaFileName","fasta"):
print( records.id )
print( records.seq ) ...
written 17 days ago by
Dattatray Mongad • 240
• updated
17 days ago by
h.mon ♦ 21k
1
vote
1
answer
105
views
1
answers
... In simple words, your idea is to take APOE gene sequence and blast it against genomes of other organisms. Using some strict BLAST output cutoffs you will manage to get estimated copy numbers of gene but not the expression levels. For measuring expression you will need microarray or transcriptome or ...
written 17 days ago by
Dattatray Mongad • 240
0
votes
1
answer
145
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1
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... The server or tool depend on your protein ids. If its UniProt ids, then you can use UniProt id conversion tool and convert them to KEGG ids. Then use KeggMapper to get the list of pathways involved. You can follow typical gene enrichmnet analysis also. ...
written 6 weeks ago by
Dattatray Mongad • 240
2
votes
2
answers
366
views
2
answers
... Core means, bacterial OTU/genera present in all samples or individuals. To do core microbiome analysis please see this [tutorial][1]
[1]: https://microbiome.github.io/microbiome/Core.html ...
written 6 weeks ago by
Dattatray Mongad • 240
0
votes
1
answer
121
views
1
answers
Answer:
A: Gut microbe annotation DB
... I am assuming you are using amplicon sequencing approach.
Currently, there is not tool or database which can tell you all information at once. Bu you can play around to gather such information.
1. Use [PICRUSt][1], to discover genes present in your data and their abundances (in terms of KO and CO ...
written 6 weeks ago by
Dattatray Mongad • 240
1
vote
1
answer
241
views
1
answers
Answer:
A: gff3 to gtf conversion
... See previous posts here [45791][1]
[1]: https://www.biostars.org/p/45791/ ...
written 6 weeks ago by
Dattatray Mongad • 240
1
vote
2
answers
214
views
2
answers
... See the link [POP][1]. You can also find some references and original scripts to generate the matrix there.
[1]: http://www.drive5.com/pop/VTML200I ...
written 8 weeks ago by
Dattatray Mongad • 240
3
votes
2
answers
214
views
2
answers
... BLOSUM and PAM series matrices are available on NCBI ftp.
See this link: ftp://ftp.ncbi.nih.gov/blast/matrices/ ...
written 8 weeks ago by
Dattatray Mongad • 240
0
votes
3
answers
2.3k
views
3
answers
... use this [Python script][1]. Easy to use: python contigPlot.py fastaDir.
Where fastaDir is directory name containing genome files (extension .fasta)
[1]: https://github.com/drdee255/code-Util/blob/master/contigPlot.py ...
written 8 weeks ago by
Dattatray Mongad • 240
0
votes
0
answers
222
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0
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... I have several microbial genomes and protein files from multiple genera. I have tried [BPGA][1] but it cantbe automated.
[1]: http://iicb.res.in/bpga/index.html ...
written 3 months ago by
Dattatray Mongad • 240
Latest awards to Dattatray Mongad
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For A: Amino Acid matrices freely downloadable url
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: Amino Acid matrices freely downloadable url
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Amino Acid matrices freely downloadable url
Scholar
4 months ago,
created an answer that has been accepted.
For A: Extract specific fasta sequences from multiple multi-fasta files located in a di
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